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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 658 by tim, Thu Jul 31 15:35:07 2003 UTC vs.
Revision 1198 by tim, Thu May 27 00:48:12 2004 UTC

# Line 4 | Line 4
4   #include <string>
5   #include <vector>
6   #include "Atom.hpp"
7 + #include "StuntDouble.hpp"
8   #include "Molecule.hpp"
9   #include "SRI.hpp"
10   #include "AbstractClasses.hpp"
# Line 12 | Line 13
13   #include "Thermo.hpp"
14   #include "ReadWrite.hpp"
15   #include "ZConsWriter.hpp"
16 + #include "Restraints.hpp"
17  
18   using namespace std;
19   const double kB = 8.31451e-7;// boltzmann constant amu*Ang^2*fs^-2/K
# Line 20 | Line 22 | const double tol = 1.0e-6;
22   const int maxIteration = 300;
23   const double tol = 1.0e-6;
24  
23 –
25   template<typename T = BaseIntegrator> class Integrator : public T {
26  
27   public:
28    Integrator( SimInfo *theInfo, ForceFields* the_ff );
29    virtual ~Integrator();
30    void integrate( void );
31 +  virtual double  getConservedQuantity(void);
32 +  virtual string getAdditionalParameters(void);
33  
31 –
34   protected:
35 <  
35 >
36    virtual void integrateStep( int calcPot, int calcStress );
37    virtual void preMove( void );
38    virtual void moveA( void );
# Line 38 | Line 40 | template<typename T = BaseIntegrator> class Integrator
40    virtual void constrainA( void );
41    virtual void constrainB( void );
42    virtual int  readyCheck( void ) { return 1; }
41 –  
42 –  void checkConstraints( void );
43 –  void rotate( int axes1, int axes2, double angle, double j[3],
44 –               double A[3][3] );
43  
44 +  virtual void resetIntegrator( void ) { }
45  
46 +  virtual void calcForce( int calcPot, int calcStress );
47 +  virtual void thermalize();
48 +
49 +  virtual bool stopIntegrator() {return false;}
50 +
51 +  virtual void rotationPropagation( StuntDouble* sd, double ji[3] );
52 +
53 +  void checkConstraints( void );
54 +  void rotate( int axes1, int axes2, double angle, double j[3],
55 +         double A[3][3] );
56 +
57    ForceFields* myFF;
58  
59    SimInfo *info; // all the info we'll ever need
60 +  vector<StuntDouble*> integrableObjects;
61    int nAtoms;  /* the number of atoms */
62    int oldAtoms;
63    Atom **atoms; /* array of atom pointers */
# Line 54 | Line 65 | template<typename T = BaseIntegrator> class Integrator
65    int nMols;
66  
67    int isConstrained; // boolean to know whether the systems contains
68 <                     // constraints.
69 <  int nConstrained;  // counter for number of constraints
70 <  int *constrainedA; // the i of a constraint pair
71 <  int *constrainedB; // the j of a constraint pair
72 <  double *constrainedDsqr; // the square of the constraint distance
73 <  
68 >         // constraints.
69 >  int nConstrained;  // counter for number of constraints
70 >  int *constrainedA; // the i of a constraint pair
71 >  int *constrainedB; // the j of a constraint pair
72 >  double *constrainedDsqr; // the square of the constraint distance
73 >
74    int* moving; // tells whether we are moving atom i
75    int* moved;  // tells whether we have moved atom i
76 <  double* oldPos; // pre constrained positions
76 >  double* oldPos; // pre constrained positions
77  
78    short isFirst; /*boolean for the first time integrate is called */
79 <  
79 >
80    double dt;
81    double dt2;
82  
83    Thermo *tStats;
84    StatWriter*  statOut;
85    DumpWriter*  dumpOut;
86 <  
86 >
87   };
88  
89   typedef Integrator<BaseIntegrator> RealIntegrator;
90  
91 + // ansi instantiation
92 + template class Integrator<BaseIntegrator>;
93 +
94   template<typename T> class NVE : public T {
95  
96   public:
97    NVE ( SimInfo *theInfo, ForceFields* the_ff ):
98      T( theInfo, the_ff ){}
99 <  virtual ~NVE(){}  
99 >  virtual ~NVE(){}
100   };
101  
102  
# Line 91 | Line 105 | template<typename T> class NVT : public T { (public)
105   public:
106  
107    NVT ( SimInfo *theInfo, ForceFields* the_ff);
108 <  virtual ~NVT() {}
108 >  virtual ~NVT();
109  
110    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
111    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
112 +  void setChiTolerance(double tol) {chiTolerance = tol;}
113 +  virtual double  getConservedQuantity(void);
114 +  virtual string getAdditionalParameters(void);
115  
116   protected:
117  
# Line 103 | Line 120 | template<typename T> class NVT : public T { (public)
120  
121    virtual int readyCheck();
122  
123 +  virtual void resetIntegrator( void );
124 +
125    // chi is a propagated degree of freedom.
126  
127    double chi;
128  
129 +  //integral of chi(t)dt
130 +  double integralOfChidt;
131 +
132    // targetTemp must be set.  tauThermostat must also be set;
133  
134    double targetTemp;
135    double tauThermostat;
136 <  
136 >
137    short int have_tau_thermostat, have_target_temp;
138  
139 +  double *oldVel;
140 +  double *oldJi;
141 +
142 +  double chiTolerance;
143 +  short int have_chi_tolerance;
144 +
145   };
146  
147  
148  
149 < template<typename T> class NPTi : public T{
149 > template<typename T> class NPT : public T{
150  
151   public:
152  
153 <  NPTi ( SimInfo *theInfo, ForceFields* the_ff);
154 <  virtual ~NPTi() {};
153 >  NPT ( SimInfo *theInfo, ForceFields* the_ff);
154 >  virtual ~NPT();
155  
156    virtual void integrateStep( int calcPot, int calcStress ){
157      calcStress = 1;
158      T::integrateStep( calcPot, calcStress );
159    }
160  
161 +  virtual double getConservedQuantity(void) = 0;
162 +  virtual string getAdditionalParameters(void) = 0;
163 +  
164 +  double myTauThermo( void ) { return tauThermostat; }
165 +  double myTauBaro( void ) { return tauBarostat; }
166 +
167    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
168    void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
169    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
170    void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
171 +  void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
172 +  void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
173 +  void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
174  
175   protected:
176  
# Line 142 | Line 179 | template<typename T> class NPTi : public T{ (protected
179  
180    virtual int readyCheck();
181  
182 <  // chi and eta are the propagated degrees of freedom
182 >  virtual void resetIntegrator( void );
183  
184 <  double chi;
185 <  double eta;
186 <  double NkBT;
184 >  virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
185 >  virtual void getVelScaleB( double sc[3], int index ) = 0;
186 >  virtual void getPosScale(double pos[3], double COM[3],
187 >                           int index, double sc[3]) = 0;
188  
189 <  // targetTemp, targetPressure, and tauBarostat must be set.  
152 <  // One of qmass or tauThermostat must be set;
189 >  virtual void calcVelScale( void ) = 0;
190  
191 <  double targetTemp;
192 <  double targetPressure;
156 <  double tauThermostat;
157 <  double tauBarostat;
191 >  virtual bool chiConverged( void );
192 >  virtual bool etaConverged( void ) = 0;
193  
194 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
195 <  short int have_target_pressure;
194 >  virtual void evolveChiA( void );
195 >  virtual void evolveEtaA( void ) = 0;
196 >  virtual void evolveChiB( void );
197 >  virtual void evolveEtaB( void ) = 0;
198  
199 < };
163 <
164 < template<typename T> class NPTim : public T{
165 <
166 < public:
167 <
168 <  NPTim ( SimInfo *theInfo, ForceFields* the_ff);
169 <  virtual ~NPTim() {};
170 <
171 <  virtual void integrateStep( int calcPot, int calcStress ){
172 <    calcStress = 1;
173 <    T::integrateStep( calcPot, calcStress );
174 <  }
175 <
176 <  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
177 <  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
178 <  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
179 <  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
180 <
181 < protected:
199 >  virtual void scaleSimBox( void ) = 0;
200  
201 <  virtual void moveA( void );
184 <  virtual void moveB( void );
201 >  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
202  
186 –  virtual int readyCheck();
187 –
188 –  Molecule* myMolecules;
189 –  Atom** myAtoms;
190 –
203    // chi and eta are the propagated degrees of freedom
204  
205 +  double oldChi;
206 +  double prevChi;
207    double chi;
194 –  double eta;
208    double NkBT;
209 +  double fkBT;
210  
211 <  // targetTemp, targetPressure, and tauBarostat must be set.  
211 >  double tt2, tb2;
212 >  double instaTemp, instaPress, instaVol;
213 >  double press[3][3];
214 >
215 >  int Nparticles;
216 >
217 >  double integralOfChidt;
218 >
219 >  // targetTemp, targetPressure, and tauBarostat must be set.
220    // One of qmass or tauThermostat must be set;
221  
222    double targetTemp;
# Line 205 | Line 227 | template<typename T> class NPTim : public T{ (protecte
227    short int have_tau_thermostat, have_tau_barostat, have_target_temp;
228    short int have_target_pressure;
229  
230 +  double *oldPos;
231 +  double *oldVel;
232 +  double *oldJi;
233 +
234 +  double chiTolerance;
235 +  short int have_chi_tolerance;
236 +  double posIterTolerance;
237 +  short int have_pos_iter_tolerance;
238 +  double etaTolerance;
239 +  short int have_eta_tolerance;
240 +
241   };
242  
243 < template<typename T> class NPTf : public T{
243 > template<typename T> class NPTi : public T{
244  
245   public:
246 +  NPTi( SimInfo *theInfo, ForceFields* the_ff);
247 +  ~NPTi();
248  
249 <  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
250 <  virtual ~NPTf() {};
249 >  virtual double getConservedQuantity(void);
250 >  virtual void resetIntegrator(void);
251 >  virtual string getAdditionalParameters(void);
252 > protected:
253  
217 –  virtual void integrateStep( int calcPot, int calcStress ){
218 –    calcStress = 1;
219 –    T::integrateStep( calcPot, calcStress );
220 –  }
254  
222 –  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
223 –  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
224 –  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
225 –  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
255  
256 < protected:
256 >  virtual void evolveEtaA(void);
257 >  virtual void evolveEtaB(void);
258  
259 <  virtual void  moveA( void );
230 <  virtual void moveB( void );
259 >  virtual bool etaConverged( void );
260  
261 <  virtual int readyCheck();
261 >  virtual void scaleSimBox( void );
262  
263 <  // chi and eta are the propagated degrees of freedom
263 >  virtual void getVelScaleA( double sc[3], double vel[3] );
264 >  virtual void getVelScaleB( double sc[3], int index );
265 >  virtual void getPosScale(double pos[3], double COM[3],
266 >                           int index, double sc[3]);
267  
268 <  double chi;
237 <  double eta[3][3];
238 <  double NkBT;
268 >  virtual void calcVelScale( void );
269  
270 <  // targetTemp, targetPressure, and tauBarostat must be set.  
271 <  // One of qmass or tauThermostat must be set;
270 >  double eta, oldEta, prevEta;
271 >  double vScale;
272 > };
273  
274 <  double targetTemp;
244 <  double targetPressure;
245 <  double tauThermostat;
246 <  double tauBarostat;
274 > template<typename T> class NPTf : public T{
275  
276 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
249 <  short int have_target_pressure;
276 > public:
277  
278 +  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
279 +  virtual ~NPTf();
280 +
281 +  virtual double getConservedQuantity(void);
282 +  virtual string getAdditionalParameters(void);
283 +  virtual void resetIntegrator(void);
284 +
285 + protected:
286 +
287 +  virtual void evolveEtaA(void);
288 +  virtual void evolveEtaB(void);
289 +
290 +  virtual bool etaConverged( void );
291 +
292 +  virtual void scaleSimBox( void );
293 +
294 +  virtual void getVelScaleA( double sc[3], double vel[3] );
295 +  virtual void getVelScaleB( double sc[3], int index );
296 +  virtual void getPosScale(double pos[3], double COM[3],
297 +                           int index, double sc[3]);
298 +
299 +  virtual void calcVelScale( void );
300 +
301 +  double eta[3][3];
302 +  double oldEta[3][3];
303 +  double prevEta[3][3];
304 +  double vScale[3][3];
305   };
306  
307 < template<typename T> class NPTfm : public T{
307 > template<typename T> class NPTxyz : public T{
308  
309   public:
310  
311 <  NPTfm ( SimInfo *theInfo, ForceFields* the_ff);
312 <  virtual ~NPTfm() {};
311 >  NPTxyz ( SimInfo *theInfo, ForceFields* the_ff);
312 >  virtual ~NPTxyz();
313  
314 <  virtual void integrateStep( int calcPot, int calcStress ){
315 <    calcStress = 1;
316 <    T::integrateStep( calcPot, calcStress );
263 <  }
314 >  virtual double getConservedQuantity(void);
315 >  virtual string getAdditionalParameters(void);
316 >  virtual void resetIntegrator(void);
317  
265 –  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
266 –  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
267 –  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
268 –  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
269 –
318   protected:
319  
320 <  virtual void  moveA( void );
321 <  virtual void moveB( void );
320 >  virtual void evolveEtaA(void);
321 >  virtual void evolveEtaB(void);
322  
323 <  virtual int readyCheck();
323 >  virtual bool etaConverged( void );
324  
325 <  Molecule* myMolecules;
278 <  Atom** myAtoms;
325 >  virtual void scaleSimBox( void );
326  
327 <  // chi and eta are the propagated degrees of freedom
327 >  virtual void getVelScaleA( double sc[3], double vel[3] );
328 >  virtual void getVelScaleB( double sc[3], int index );
329 >  virtual void getPosScale(double pos[3], double COM[3],
330 >                           int index, double sc[3]);
331  
332 <  double chi;
332 >  virtual void calcVelScale( void );
333 >
334    double eta[3][3];
335 <  double NkBT;
335 >  double oldEta[3][3];
336 >  double prevEta[3][3];
337 >  double vScale[3][3];
338 > };
339  
286 –  // targetTemp, targetPressure, and tauBarostat must be set.  
287 –  // One of qmass or tauThermostat must be set;
340  
341 <  double targetTemp;
290 <  double targetPressure;
291 <  double tauThermostat;
292 <  double tauBarostat;
341 > template<typename T> class ZConstraint : public T {
342  
343 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
344 <  short int have_target_pressure;
343 >  public:
344 >  class ForceSubtractionPolicy{
345 >    public:
346 >      ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
347  
348 < };
348 >      virtual void update() = 0;
349 >      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
350 >      virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
351 >      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
352 >      virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
353  
354 < template<typename T> class ZConstraint : public T {
354 >   protected:
355 >     ZConstraint<T>* zconsIntegrator;
356 >  };
357  
358 +  class PolicyByNumber : public ForceSubtractionPolicy{
359 +
360 +    public:
361 +      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
362 +      virtual void update();
363 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
364 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
365 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
366 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
367 +
368 +    private:
369 +      int totNumOfMovingAtoms;
370 +  };
371 +
372 +  class PolicyByMass : public ForceSubtractionPolicy{
373 +
374 +    public:
375 +      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
376 +
377 +      virtual void update();
378 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
379 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
380 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
381 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
382 +
383 +   private:
384 +     double totMassOfMovingAtoms;
385 +  };
386 +
387   public:
388  
389    ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
390    ~ZConstraint();
391  
306 –  virtual void integrateStep( int calcPot, int calcStress );
307 –  
308 –  
392    void setZConsTime(double time)                  {this->zconsTime = time;}
393    void getZConsTime()                             {return zconsTime;}
394 <  
395 <  void setIndexOfAllZConsMols(vector<int> index)  {indexOfAllZConsMols = index;}
396 <  void getIndexOfAllZConsMols()                   {return indexOfAllZConsMols;}
397 <  
398 <  void setZConsOutput(const char * fileName)      {zconsOutput = fileName;}
394 >
395 >  void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
396 >  void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
397 >
398 >  void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
399    string getZConsOutput()                         {return zconsOutput;}
400  
401 +  virtual void integrate();
402 +
403 +
404   #ifdef IS_MPI
405 <  virtual void update(); //which is called to indicate the molecules' migration
405 >  virtual void update();                      //which is called to indicate the molecules' migration
406   #endif
407  
408 +  enum ZConsState {zcsMoving, zcsFixed};
409 +
410 +  vector<Molecule*> zconsMols;              //z-constraint molecules array
411 +  vector<ZConsState> states;                 //state of z-constraint molecules
412 +
413 +
414 +
415 +  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
416 +  double totalMassOfUncons;                //total mas of unconstraint molecules
417 +
418 +
419   protected:
420  
324 –  double zconsTime;
325 –  
326 –  void resetZ(void);
327 –  
328 –  vector<Molecule*> zconsMols;
329 –  vector<double> massOfZConsMols;
330 –  
331 –  vector<Molecule*> unconsMols;
332 –  vector<double> massOfUnconsMols;
333 –  double totalMassOfUncons;
421  
422 <  vector<double> allRefZ;    
423 <  vector<double> refZ;
424 <  
422 >
423 >  virtual void calcForce( int calcPot, int calcStress );
424 >  virtual void thermalize(void);
425 >
426 >  void zeroOutVel();
427 >  void doZconstraintForce();
428 >  void doHarmonic(vector<double>& resPos);
429 >  bool checkZConsState();
430 >
431 >  bool haveFixedZMols();
432 >  bool haveMovingZMols();
433 >
434 >  double calcZSys();
435 >
436 >  int isZConstraintMol(Molecule* mol);
437 >
438 >
439 >  double zconsTime;                              //sample time
440 >  double zconsTol;                                 //tolerance of z-contratint
441 >  double zForceConst;                           //base force constant term
442 >                                                          //which is estimate by OOPSE
443 >
444 >
445 >  vector<double> massOfZConsMols;       //mass of z-constraint molecule
446 >  vector<double> kz;                              //force constant array
447 >
448 >  vector<double> zPos;                          //
449 >
450 >
451 >  vector<Molecule*> unconsMols;           //unconstraint molecules array
452 >  vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
453 >
454 >
455 >  vector<ZConsParaItem>* parameters; //
456 >
457    vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
458 <  int* indexOfZConsMols;               //index of local Z-Constraint Molecules
459 <    
460 <  double* fz;
458 >
459 >  vector<int> indexOfZConsMols;                   //index of local Z-Constraint Molecules
460 >  vector<double> fz;
461 >  vector<double> curZPos;
462 >
463 >  bool usingSMD;
464 >  vector<double> prevCantPos;
465 >  vector<double> cantPos;
466 >  vector<double> cantVel;
467 >
468 >  double zconsFixTime;  
469 >  double zconsGap;
470 >  bool hasZConsGap;
471 >  vector<double> endFixTime;
472    
473 +  int whichDirection;                           //constraint direction
474 +
475   private:
476  
477 <  int isZConstraintMol(Molecule* mol);
478 <  string zconsOutput;
479 <  ZConsWriter* fzOut;
477 >  string zconsOutput;                         //filename of zconstraint output
478 >  ZConsWriter* fzOut;                         //z-constraint writer
479 >
480 >  double curZconsTime;
481 >
482 >  double calcMovingMolsCOMVel();
483 >  double calcSysCOMVel();
484 >  double calcTotalForce();
485 >  void updateZPos();
486 >  void updateCantPos();
487 >  
488 >  ForceSubtractionPolicy* forcePolicy; //force subtraction policy
489 >  friend class ForceSubtractionPolicy;
490 >
491   };
492  
493   #endif

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